Research workbench
Structure of PTP1B in complex with a peptidic bisphosphonate inhibitor
Analyse Structure of PTP1B in complex with a peptidic bisphosphonate inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LQF
- Type
- protein
- Length
- 1,148 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-tyrosine phosphatase, non-receptor type 1
- EC
- 3.1.3.48
- UniProt
- P18031
- Ligands
- BGD
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein-tyrosine phosphatase, non-receptor type 1 (EC 3.1.3.48) | protein | 287 | 36% helix, 22% strand | P18031 |
Ligands and binding sites
- BGD · N-benzoyl-L-glutamyl-[4-phosphono(difluoromethyl)]-L-phenylalanine-[4-phosphono(difluoro-methyl)]-L-phenylalanineamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.82 | 0.84 | 71 | empty |
| 2 | 475 | 0.76 | 0.84 | 37 | empty |
| 3 | 410 | 0.75 | 0.85 | 38 | empty |
| 4 | 355 | 0.72 | 0.84 | 26 | empty |
| 5 | 429 | 0.72 | 0.82 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–D · 813 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 638 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 311 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 189 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1LQF · Structure of PTP1b in Complex with a Peptidic Bisphosphonate Inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P18031
- Elsewhere: RCSB PDB 1LQF · PDBe 1LQF · UniProt P18031
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